Your brand filter is very temperamental. Even after updating permalinks, some work and some give 404 error message. It happens ever so randomly and also may I ask why are you using jquery to submit a “?brand=brand%20name” value to a page to work out which page it needs to redirect to and then wordpress doing a 301 redirect to the correct page /brand/brand-name ? When /brand/brand-name is already a valid page in the first place that you can link directly to?
Why not get jquery to redirect directly to the correct link to the correct page /brand/brand-name without all this submitting values, recalculating and redirecting using 301’s?
Can you not get wordpress to work out the type of permalink it is using and attach the full link instead. Avoids all the issues, 301 redirects etc
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And another brand issue, if you set up a parent>child, the parent brand does not get recognized as a taxonomy to pass the woocommerce_products_will_display() check and therefore the page does not display the filter search options.
The piece of code your theme fails on is at woocommerce/archive-product.php